3D, 2D and 1D networks via N-H... O and N-H... N hydrogen bonding by the bis-amide analogues: Effect of chain lengths and odd-even spacers

Article abstract of DOI:10.1007/s12039-014-0696-7

The synthesis, crystal structures and hydrogen bonding networks of four members of the bis(pyridinecarboxamido)alkane and bis(pyridyl)alkanediamides series (1 ≈ n ; 8), where the amide moieties are separated by alkyl chain (-(CH₂)_n-) having even or odd number of -(CH₂)-groups are explored and correlated with the previously reported structures. The odd members (n = odd) of both the series are found to adopt three-dimensional networks in contrast to the 1D or 2D structures of the even members (n = even). This odd-even effect on the dimensionality of the networks however disappears with increase in chain length.

Full text of DOI:10.1007/s12039-014-0696-7

J. Chem. Sci. Vol. 126, No. 5, September 2014, pp. 1285–1290. ꢀc Indian Academy of Sciences.
3
D, 2D and 1D networks via N-H· · · O and N-H· · · N hydrogen bonding
by the bis-amide analogues: Effect of chain lengths and odd-even spacers
∗
GARGI MUKHERJEE and KUMAR BIRADHA
Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India
e-mail: kbiradha@chem.iitkgp.ernet.in
MS received 17 June 2014; revised 9 July 2014; accepted 12 July 2014
Abstract. The synthesis, crystal structures and hydrogen bonding networks of four members of the
bis(pyridinecarboxamido)alkane and bis(pyridyl)alkanediamides series (1≤ n≤ 8), where the amide moieties
are separated by alkyl chain (-(CH2)n-) having even or odd number of -(CH2)-groups are explored and cor-
related with the previously reported structures. The odd members (n= odd) of both the series are found to
adopt three-dimensional networks in contrast to the 1D or 2D structures of the even members (n= even). This
odd-even effect on the dimensionality of the networks however disappears with increase in chain length.
Keywords. Odd-even effect; amide-to-amide hydrogen bond; pyridine interferences; organic diamondoid.
1
. Introduction
via amide-to-amide recognitions while pyridine inter-
ferences to amide-to-amide hydrogen bond is more
prominent in case of reverse amide series (3 and 4), i.e.,
N-H· · · N interaction is preferred over N-H· · · O hydro-
gen bond. In contrast to the 1D or 2D structures of the
even ones, 3D structures are more regular in case of
odd ones. To confirm the trend, in this report we have
synthesized four more derivatives of both the series
including the higher ends and crystallized them. The
crystal structures and preference for amide-to-amide
hydrogen bonding is analyzed in comparison with
the previously reported structures.
Various types of intermolecular interactions, in par-
ticular the hydrogen bonding interactions between the
functional groups of the molecules, result in the for-
mation of different types of networks.1 The predic-
tion of these supramolecular networks depends on the
information that lies in the functional groups, which
are present in the molecules, and the identification
of the supramolecular synthons between those func-
tional groups. The preference for one supramolecu-
lar synthon over the other depends on the combina-
tion of various factors such as energetic, steric and
solvation of the functional groups. The formation of
the final supramolecular array in a crystal is a result
of the balance between all the intermolecular interac-
tions and the geometry of the molecules. Recently, we
have explored the crystal structures of two homologous
series of bis(pyridinecarboxamido)alkane (amide) and
–3
2. Experimental
2.1 Materials
All the reagents and solvents employed were com-
mercially available and used as supplied with-
out further purification. Triphenylphosphite and
pyridine were obtained from Merck Co. Azeloyl
chloride, nicotinamide, 3-pyridinecarboxylic acid
and 4-pyridinecarboxylic acid were obtained from
Aldrich Co. α, ω-diamino alkanes, 3-aminopyridine,
4
bis(pyridyl)alkanediamides (reverse amide) (scheme 1).
Our previous studies revealed that both the series show
the odd-even effect on the nature of hydrogen bond
5
and their network features. As the derivatives con-
tain two amide moieties and two pyridine units, the
molecules can be assembled through either N-H· · · O
4-aminopyridine and formaldehyde solution were
6
or N-H· · · N or both the interactions. The β-sheets
obtained from Spectrochem-India.
7
or (4,4) networks formed by N-H· · · O or N-H· · · N
hydrogen bond, are the two most common motifs dis-
played by the even members of the amide series.
The amide molecules (1 and 2) are assembled mostly
2.2 Physical measurements
1H NMR (200 MHz) spectra were recorded on a
Bruker-AC spectrometer at room temperature Ele-
mental analyses were obtained with a Perkin Elmer
∗
For correspondence
1
285

1
286
Gargi Mukherjee and Kumar Biradha
◦
O
O
H
N
H
N
200 C to yield 1a. The product was recrystallized from
hot water. Diffractable quality crystals were obtained
from DMF.
(
CH
2
)n
N
(CH
)n
2
R
N
H
R
R
R
H
O
O
◦
1
a, Yield = 73%, M.p 235–240 C. Anal. Calcd for
3
: R= 3-pyridyl, 4: R= 4-pyridyl
1
: R= 3-pyridyl, 2: R= 4-pyridyl
a) n = 1 (b) n = 3 (c) n = 5 (d) n= 7
e) n = 2 (f) n = 4 (g) n= 8 (h) n = 8
C H N O : C, 60.93%; H, 4.72%; N, 21.86%; Found:
13
12
4
2
(
C, 61.65%; H, 4.33%; N, 21.98%.
(
Scheme 1. Schematic presentation of amide derivatives.
2.3b Procedure for synthesis of 2c and 2d: The
derivatives 2c and 2d were synthesized by the follow-
ing procedure. To a solution of 4-pyridinecarboxylic
acid (4 g, 1 mmol) in pyridine (40 mL) was added cor-
responding α, ω-diaminoalkane (2 mmol). The solution
was stirred for 15 min and triphenyl phosphite (9 mL,
instrument, series II, CHNS/O analyzer 2400. Melt-
ing point measurement was carried out using Fisher
Scientific instrument Cat. No. 12-144-1.
2
mmol) was added slowly. The mixture was refluxed
The single crystal data was collected on Bruker
APEX-2 CCD X-ray diffractometer that uses graphite
monochromated MoKα radiation (λ = 0.71073 Å)
by hemisphere method. The structures are solved
by direct methods and refined by least square methods
◦
for 4 h at 100 C in an oil bath. A brown solution
resulted, which after volume reduction yielded a brown
oil. This was taken up in chloroform (10 mL), washed
three times with water, four times with saturated sodium
bicarbonate solution, and then again three times with
water. The resulting chloroform solution was dried over
sodium sulfate and concentrated. 30 mL of ice-cold
diethyl ether was added dropwise to the concentrated
light brown. The mixture was stirred in an ice bath for
2
9
on F using SHELX-97. Non-hydrogen atoms were
refined anisotropically and hydrogen atoms were fixed
at calculated positions and refined using a riding
model.
1
h. The white solid obtained was dried and recrystal-
lized. 2c and 2d were crystallized from (1:1) mixture
of methanol-toluene and methanol-DMSO solutions,
respectively.
2
.3 Synthetic procedures
2.3a Procedure for synthesis of 1a: Nicoti-
namide suspended in 35% neutralized formalde-
◦
◦
hyde solution was refluxed for an hour at 100 C, 2c, Yield = 40%, M.p 120–124 C. Anal. Calcd for
cooled and recrystallized from acetone to yield N- C H N O : C, 58.61%; H, 6.94%; N, 16.08%; Found:
17
24
4
2
hydroxymethylnicotinamide. This solid was heated at C, 58.56%; H, 6.89%; N, 15.88%.
Table 1. Crystallographic parameters for 1a, 2c, 2d and 3d.
Molecules
1a
2c
2d
3d
Formula
Mol.Wt.
T (K)
C13H12N4O2
256.27
C17H24N4O4
348.40
C19H24N4O2
340.42
C38H48N8O4
680.84
293(2)
296(2)
293(2)
293(2)
System
Space Group
a(Å)
Orthorhombic
Monoclinic
Monoclinic
Triclinic
P-1
Fdd2
C2/c
P21/c
20.679(7)
28.501(10)
4.1182(15)
90.00
90.00
90.00
2427.1(15)
8
17.7550(12)
9.1736(7)
14.2042(16)
90.00
4.8639(5)
18.3835(19)
20.485(2)
90.00
96.746(4)
90.00
1819.0(3)
4
1.243
0.0744
0.2397
4.715(4)
10.493(8)
19.088(14)
102.52(3)
93.32(3)
95.97(3)
913.6(12)
1
b(Å)
c(Å)
α( )
◦
◦
β( )
126.398(3)
◦
γ ( )
90.00
1862.2(3)
4
1.243
0.0426
V (Å3)
Z
D(g/cm3)
R1(I > 2σ(I))
1.403
0.0387
0.0563
1.237
0.0773
0.2400
2
wR2(on F , all data)
0.0622

Effect of chain lengths and odd-even spacers on h-bonding
1287
Table 2. Geometrical parameters of hydrogen bonds in 1a, 2c, 2d and 3d.
Molecules
Type
H· · · A (Å)
D· · · A (Å)
D-H· · · A (◦)
1
2
2
a
c
N-H· · · N
C-H· · · O
2.26
2.37
3.035(3)
3.245(3)
150
156
N-H· · · O(W)
2.08
2.04
2.830(3)
2.874(3)
159
166
O(W)-H· · · N
N-H· · · O
N-H· · · O
C-H· · · O
N-H· · · N
N-H· · · O
C-H· · · O
d
2.03
1.99
2.57
2.808(5)
2.821(5)
3.208(7)
150
161
127
3
d
2.18
2.04
2.48
3.017(7)
2.892(6)
3.365(8)
164
170
151
◦
◦
2
d, Yield = 52%, M.p 125–127 C. Anal. Calcd for triethylamine (2 mmol) was cooled to 0 C under nitro-
C H N O : C, 67.04%; H, 7.11%; N, 16.46%; Found: gen atmosphere and to this solution azeloyl chloride
19
24
4
2
C, 67.32%; H, 7.54%; N, 16.23%.
(1 mmol) in THF was added drop wise with continuous
stirring. The solution was stirred overnight. THF was
2
.3c Procedure for synthesis of 3d: Tetrahydrofuran distilled off and the resulting solid was washed three
(
THF) solution of 3-aminopyridine (2 mmol) and times with water and dried under vacuum.
Figure 1. Illustrations for the crystal structure of 1a: Molecular geometry of (a) 1a,
(
b) fourfold helix via N-H· · · N hydrogen bonds (top view) (c) tetrahedral node forma-
tion, (d) single supramolecular adamantanoid cage, and (e) three-fold interpenetrated
adamantanoid network; the central C-atom of alkyl spacer was considered as a node.

1
288
Gargi Mukherjee and Kumar Biradha
◦
3
d, Yield = 65%, M.p 155–160 C. Anal. Calcd for derivatives of 1a, 2c, 2d and 3d are given in tables 1 and
C H N O : C, 67.04%; H, 7.11%; N, 16.46%; Found: 2, respectively.
19
24
4
2
C, 66.83%; H, 7.92%; N, 16.98%.
Molecule 1a crystallizes in orthorhombic space
group Fdd2 and the asymmetric unit is composed of
half unit of molecule 1a. Interestingly, the molecule
exhibits arclike geometry as observed previously with
other members of the bis-amide series having odd num-
3. Results and Discussion
The molecule 1a, 2c, 2d and 3d (scheme 1) were syn- ber of alkyl chain (figure 1). The amide groups and
thesized by employing two well known procedures of the pyridyl N are aligned trans to each other mak-
amide syntheses. The amide derivatives (1a, 2c and ing the molecule to act as 4-connected node. Desig-
2
d) were prepared by the reaction of corresponding nating the molecule as node and hydrogen bond as
α, ω-alkanediamines with pyridine acid in the presence nodal connection revealed that the network exhibits
of pyridine and triphenylphosphite, while the reverse diamondoid topology. The diamondoid units are com-
amide derivative (3d) was prepared by the coupling posed of two distances 9.322 and 9.336 Å, respec-
of α, ω-alkanediacid chlorides and the corresponding tively. The molecules are assembled exclusively by
amine. The crystallizations of molecules 1a, 2c, 2d N-H· · · N interactions in a four-fold helical fashion to
and 3d in various solvents resulted in single crys- form a three-dimensional network and the voids are
tals suitable for X-ray diffraction. In this contribu- filled through three-fold interpenetration. The interpen-
tion, the crystal structures of 1a, 2c, 2d and 3d will etration occurs through aromatic interactions of pyridyl
be analyzed in comparison to the previously reported rings. This structure bears a striking resemblance with
structures of both amide and reverse amide deriva- previously reported organic diamondoid network of
tives. Molecule 1a exhibits three-fold interpenetrated bis(4-pyridinecarboxamido)methane, (4a) which exhib-
8
diamondoid network. 2c is found to include water ited four-fold interpenetration in contrast to the three-
molecule and afforded a tubular network. 2d forms hon- fold interpenetration observed here. Despite similar arm
eycomb network supported by amide-to-amide recog- length (∼9.3 Å) of diamondoid networks, the change in
nition and 3d exhibits 1D- network based on alter- four-fold to three-fold interpenetration could be due to
nate N-H· · · O and N-H· · · N interactions. The pertinent the differences in the geometry of the molecules which
crystallographic details and geometrical parameters of ultimately fill the voids. Also, in the present one the
strong hydrogen bonds involving amide functionality of tetrahedral node is found to be more distorted compared
Figure 2. Illustrations for the crystal structure of 2c: Molecular geometry of (a) 2c,
(
b) tubular structure, and (c) hydrogen bonding between the tubes by water molecules.

Effect of chain lengths and odd-even spacers on h-bonding
1289
to the previous one. The angles of the tetrahedral con- that previously four water molecules were observed to
◦
◦
◦
nection in 1a vary from 80 to 140 in contrast to 102
to 125 in case of 4a.
be connected with each ligand in contrast to six water
molecules per ligand here.
◦
Molecule 2c also exhibits a twisted geometry and
In contrast to molecules 1a and 2c, molecule 2d is
crystallizes in monoclinic space group C2/c as hydrate. assembled exclusively via N-H· · · O interaction which
The asymmetric unit is composed of half unit of is the first example of occurrence of amide-to-amide
molecule 2c and one unit of water molecule. This recognition in this series having odd number of alkyl
structure is the only example of inclusion of water chain derivatives. The molecule 2d crystallizes in mon-
molecule in crystal lattices out of nine bis-amide deriva- oclinic space group P 2 /c. Each molecule connects
1
tives having odd number of -(CH ) - studied (figure 2). with three other molecules through four N-H· · · O
2
n
Water molecules exhibit 3-centred hydrogen bonding interactions and an unique (6,3) network is observed
interactions, one each with amide CO, amide NH (figure 3). The geometry of the network is honeycomb
and pyridine N-atom from three different molecules, with arm lengths 4.338 and 11.561 Å. It is to be noted
whereas the molecule 2c is engaged in hydrogen bond here that previously in the case of even spacer amide
with six water molecules through two each of pyridine derivatives (1f, 2f), 2D layer with (4,4) topology was
N-atoms, amide CO, amide NH, leads to a tubular struc- observed.
ture. These tubular units further interact with each other
The molecule 3d bears iso-structurality with the
through water molecules. It is to note here that previ- bis(3-pyridyl)alkanediamides having six (3g) and eight
ously the bis(4-pyridyl)alkanediamides (reverse amide) (3h) spacers and all the three homologous molecules
derivatives with (CH ) (4g) and (CH ) (4h) were crystallize in identical space group P -1 (figure 4). How-
2
6
2 8
found to flaunt similar types of tubular structure with ever there is a subtle difference in geometry of lig-
inclusion of water molecules, the only difference is ands. The angle between the amide plane and pyridine
◦
◦
plane (θ) for molecule 3d are 6.99 and 5.90 whereas
◦
◦
◦
those for 3g are 33.4 and 26.5 and for 3h are 27.9
◦
and 4.3 , respectively. Despite large differences in θ
values, the trio exhibit similar hydrogen bonding pat-
tern in which the molecules are assembled via alternate
N-H· · · O and N-H· · · N interactions and results a 1 D
network.
Figure 3. Illustrations for the crystal structure of 2d:
Molecular geometry of (a) 2d, (b) formation of 2D layer
via amide-to-amide hydrogen bonds, and (c) honeycomb Figure 4. Illustrations for the crystal structure of 3d:
network through connection of the central C-atom of alkyl Molecular geometry of (a) 3d, and (b) formation of 1D chain
spacer considered as a node.
via amide-to-amide hydrogen bonds.

1
290
. Conclusions
Gargi Mukherjee and Kumar Biradha
4
References
1
2
3
. (a) Desiraju G R and Steiner T 1999 In The weak hydro-
gen bond in structural chemistry and biology (Oxford:
Oxford University Press); (b) Zaworotko M J 2001 Chem.
Commun. p1
. (a) Desiraju G R 1989 In Crystal Engineering: The design
of organic solids (Amsterdam: Elsevier); (b) Desiraju
G R 1995 Angew. Chem. Int. Ed. 34 2311; (c) Etter M C
In our previous studies on the homologous series
of bis(pyridinecarboxamido)alkane (amide) and
bis(pyridyl)alkanediamides (reverse amide), it was
shown that the odd members display more propensi-
ties to adopt 3-dimensional structures compared to the
even ones and reverse amides show greater tendencies
to exhibit pyridine interferences in amide-to-amide
hydrogen bonding, i.e., N-H· · · N hydrogen bond is
more prevalent. However, structural studies on the
higher analogues of series show that the odd-even
alteration of dimensionality of network and hydrogen
bonding patterns gradually fades away with increase
in chain length. The lower analogues (n = 1, 3, 5) of
the series mainly exhibits diamondoid or quartz type
topology formed by N-H· · · N hydrogen bond. But in
case of seven membered (n = 7) derivatives of both the
series, we see that either 1D or 2D network is exhib-
ited. Further, pyridine interference in amide-to-amide
hydrogen bonding reduces and N-H· · · O interactions
play more important role in assembling the network
as we observed earlier in case of even analogues. For
example, molecule 2d of amide series has 2D net-
work and 3d of reverse amide series has 1D structure
which is iso-structural with its even member analogues
1
990 Acc. Chem. Res. 23 120
. (a) Nguyen T L, Fowler F W and Lauher J W 2001 J.
Am. Chem. Soc. 123 11057; (b) Das D and Desiraju G R
2
006 Chem. Asian J. 1 231; (c) Bis J A, Vishweshwar P,
Middleton R A and Zaworotko M J 2006 Cryst. Growth
Des. 6 1048
4
5
. (a) Sarkar M and Biradha K 2006 Cryst. Growth Des.
6
202; (b) Rajput L, Singha S and Biradha K 2007
Cryst. Growth Des. 7 2788; (c) Mukherjee G and Biradha
K 2011 Cryst. Growth Des. 11 924; (d) Sarkar M and
Biradha K 2005 Chem. Commun. 2229; (e) Biradha K and
Rajput L 2010 In Organic crystal engineering: Frontiers
in crystal engineering E R T Tiekink, J J Vittal and M J
Zaworotko (Eds.) (Chichester: John Wiley Publishers)
. (a) Boese R, Weiss H-C and Bläser D 1999 Angew. Chem.
Int. Ed. 38 988; (b) Thalladi V R, Boese R and Weiss H-C
2
000 J. Am. Chem. Soc. 122 1186; (c) Thalladi V R,
Boese R and Weiss H-C 2000 Angew. Chem. Int. Ed. 39
918; (d) Thalladi V R, Nüsse M and Boese R 2000 J. Am.
Chem. Soc. 122 9227
6
7
. (a) Lauher J W, Chang Y L and Fowler F W 1992 Mol.
Cryst. Liq. Cryst. 211 99; (b) Zhao Y L and Wu Y D 2002
J. Am. Chem. Soc. 124 2002
. Batten S R and Robson R 1998 Angew. Chem. Int. Ed. 37
1460
having -(CH )-group one less (n = 6, 3g) or one more
2
(
n = 8, 3h). Although there are only two crystal struc-
tures with higher spacers, the structural trend is pretty
clear from these structures.
8. (a) Craig D C, Dance I G and Garbutt R 1986 Angew.
Chem. Int. Ed. Engl. 25 165; (b) Ermer O 1988 J. Am.
Chem. Soc. 110 3747; (c) Ermer O and Eling A 1988
Angew. Chem. Int. Ed. Engl. 27 829; (d) Hoskins B F and
Robson R 1990 J. Am. Chem. Soc. 112 1546; (e) Simard
M, Su D and Wuest J D 1991 J. Am. Chem. Soc. 113 4696;
Supplementary Information
The electronic supporting information can be seen at
www.ias.ac.in/chemsci.
(
f) Copp S B, Subramanian S and Zaworotko M J 1992
J. Am. Chem. Soc. 114 8719; (g) Brunet P, Simard M and
Wuest J D 1997 J. Am. Chem. Soc. 119 2737; (h) Reddy
D S, Dewa T, Endo K and Aoyama Y 2000 Angew. Chem.
Int. Ed. 39 4266; (i) Men Y B, Sun J, Huang Z-T and
Zheng Q Y 2009 CrystEngComm 11 978
. Sheldrick G M 1997 In Program for the Solution and
Refinement of Crystal Structures, SHELX-97 (Germany:
University of Gottingen)
Acknowledgements
We gratefully acknowledge the DST for financial sup-
port and DST-FIST for single crystal diffractometer.
GM thanks CSIR for a research fellowship.
9